I don't think it was the fault of Nintendo for this decision.
In all seriousness, do remember that people create their own realities (you know how it is with getting jinxed), so try not to talk or think about it too much. The chances that either Reborn or Rejuvenation get taken down are relatively slim as they haven't drawn even half the attention that Uranium got, as well as their popularity having gradually risen rather than Uranium's popularity having spiked in 2-3 days.
And as someone who's making a game as well, I'm also taking a risk by making a fangame as making one is in a very grey zone of fanworks of something, so when deciding to make one, it's very much possible that my game gets a takedown notice as well. This is a risk that a game creator takes and accepts to take from the moment they start working on it. Refusing to accept these risks is simply a matter of not being ready or able to face the consequences if a similar situation as Uranium happens.
Jan knows about this, Ame knows about this, and if it ever does occur that the game gets a takedown notice, they'll be fully prepared for it. But right now as things are, the chances that these games get taken down is just very, very small, so it's better to not worry and think about it all the time until the time comes that there's a popularity spike.